Nats leadership overshadows parliament

The Turnbull government is hoping to move on from the Barnaby Joyce affair when parliament resumes on Monday, but Labor is unlikely to ease the pressure on the bruised coalition.

Mr Joyce resigned on Friday after a fortnight of relentless media and political scrutiny over his extra-marital relationship with former media adviser Vikki Campion, who is now pregnant with his child.

The Nationals party room will meet at 8am AEDT on Monday to determine who will replace Mr Joyce and become deputy prime minister, with their choice of ministerial portfolio.

Veteran Affairs Minister Michael McCormack is likely to win. David Gillespie withdrew on Sunday, while Agricutlure Minister David Littleproud is reportedly still considering his position.

Prime Minister Malcolm Turnbull returns to parliament from Washington early on Monday to start work with his new deputy to rebuild the government's fortunes which have been battered by the handling of the Joyce affair.

A Sky News/ReachTEL poll on Sunday had Mr Turnbull's and the government's approval ratings slipping.

The new Nationals leader will face his first question time test, with Labor expected to zero in on the secrecy behind the coalition agreement - a private letter exchanged between the Nationals and Liberals leaders which forms the basis of how they work together.

Senator McKenzie said the agreement was "not some sacred document" but administrative details of how the parties would form government.

"The Governor-General is across it. That's all that we need to worry about," she said.

The Governor-General's official secretary told senators shortly after the 2016 election the Queen's representative had not been given a copy of the agreement.

The federal opposition is still also interested in whether Mr Joyce breached any ministerial standards, or expenses guidelines, over his affair with Ms Campion.

Labor will also exploit the battle between Tony Abbott and his former cabinet colleagues.

The former prime minister has used the parliamentary break to criticise ministers over their support for higher migration, and says the Joyce affair has been poorly managed "at the most senior levels of government".

Meanwhile, Senate estimates hearings will probe ministers and senior officials from government agencies and departments.

Key issues to be explored will be the cost of health care, defence exports, offshore detention, the rollout of the new Home Affairs portfolio and controversial changes to the Murray Darling Basin Plan.